Amino Acid Encryption Method Using Genetic Algorithm for Key Generation
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Computers, Materials & Continua Tech Science Press
DOI:10.32604/cmc.2022.019455
Article
Amino Acid Encryption Method Using Genetic Algorithm for Key Generation
Ahmed S. Sakr1 , M. Y. Shams2 , Amena Mahmoud3 and Mohammed Zidan4, *
1
Department of Information System, Faculty of Computers and Information, Menofia University, Egypt
2
Department of Machine learning and Information Retrieval, Faculty of Artificial Intelligence,
Kafrelsheikh University, Egypt
3
Department of Computer Science, Faculty of Computers and Information, Kafrelshiekh University, Egypt
4
Hurghada Faculty of Computers and Artificial Intelligence, South Valley University, Egypt
*
Corresponding Author: Mohammed Zidan. Email: comsi2014@gmail.com
Received: 13 April 2021; Accepted: 14 May 2021
Abstract: In this new information era, the transfer of data and information
has become a very important matter. Transferred data must be kept secured
from unauthorized persons using cryptography. The science of cryptography
depends not only on complex mathematical models but also on encryption
keys. Amino acid encryption is a promising model for data security. In this
paper, we propose an amino acid encryption model with two encryption keys.
The first key is generated randomly using the genetic algorithm. The second
key is called the protein key which is generated from converting DNA to a
protein message. Then, the protein message and the first key are used in the
modified Playfair matrix to generate the cypher message. The experimental
results show that the proposed model survives against known attacks such
as the Brute-force attack and the Ciphertext-only attack. In addition, the
proposed model has been tested over different types of characters including
white spaces and special characters, as all the data is encoded to 8-bit binary.
The performance of the proposed model is compared with other models
using encryption time and decryption time. The model also balances all three
principles in the CIA triad.
Keywords: Cryptography; amino acid; genetic algorithm; playfair; deep
learning; DNA computing
1 Introduction
Internet and wireless networks offer ubiquitous channels to deliver and exchange data. Some
models, such as cryptography, are used to improve the security of data transfer. Cryptography
keeps data secure by ensuring that it is not understandable to unauthorized persons. There are
two types of encryption: symmetric and asymmetric.
In cryptography, messages are scrambled and become gibberish to help ensure their secrecy.
Once a message is encrypted, everyone can see that there is a message, but it cannot be understood
This work is licensed under a Creative Commons Attribution 4.0 International License,
which permits unrestricted use, distribution, and reproduction in any medium, provided
the original work is properly cited.
124 CMC, 2022, vol.70, no.1
or read by anyone who does not have the decryption key. As a result, decryption keys must be very
difficult to access and use, so that only the intended recipients can read encrypted messages [1–3].
One potential model for key generation is the use of Genetic Algorithms (GA) [4]. Genetic
Algorithms are based on Darwin’s theory of natural selection and “survival of the fittest.” Genetic
Algorithms are used to search among many solutions and find the optimal one. This model
depends on randomly selecting several solutions and calculating how good each solution is. Each
solution is represented by a chromosome. To calculate each solution’s degree and rank, a fitness
function is used. A generation consists of a number of chromosomes. After calculating the fitness
function for each suggested solution (chromosome) a generation is finished. A portion of the
chromosomes is selected to be part of the next generation. New chromosomes are generated by
applying crossover and mutation functions. (The best chromosomes generate the best results.)
After that, the old selected chromosomes and the newly generated ones are combined to construct
the new generation. These iterations continue until a pre-defined threshold is reached. In the
end, the best solution is selected for the minimization or maximization function. The solution
consists of the best chromosome that achieves the best results for the objective function [5–7].
The encryption system then uses machine learning and DNA-based encryption to improve secu-
rity. DNA-based encryption is an emerging approach for information security because of its
capabilities.
In biology, DNA is the master molecule whose structure encodes all the information needed
to create and direct the chemical machinery of life. In 1953, the structure of DNA was correctly
predicted by Watson and Crick. They predicted that DNA molecules consist of two long polynu-
cleotide chains. Each of these chains is known as a DNA chain, or a DNA strand, which is made
up of simple subunits, called nucleotides. Each nucleotide consists of a sugar-phosphate molecule
with a nitrogen-containing side group, or base. The bases are of four types—adenine, guanine,
cytosine, and thymine—corresponding to four distinct nucleotides, labeled A, G, C, and T [8–14].
In the proposed model, Genetic Algorithms are used to generate a random key for encryption
and decryption. The generated key is used to encrypt data using DNA encryption.
The rest of this paper is organized as follows: first we discuss a review of related work, next
we explain the proposed model, then we report the simulation results and performance analysis,
and finally we discuss the conclusions and future work.
2 Literature Review
In [15] the authors significantly modify the old Playfair cipher by introducing a DNA-based
and amino acid structure. In their work a plain message is converted to a sequence of DNA.
They propose assigning each letter of the alphabet a corresponding codon, so that the English
alphabet’s form of amino acids can go through the traditional Playfair cipher process using the
secret key.
In [16], the authors propose a novel algorithm that is composed of encryption and steganog-
raphy using (DNA) sequences. Their model consists of two phases. In the first phase, the plain
data is encrypted using a DNA-and amino acids-based Playfair cipher. In the second phase, the
encrypted data is inserted into a DNA sequence. Their algorithm works on any binary data as it
is transformed into DNA nucleotides. Then, these DNA nucleotides are converted to the amino
acids structure so that they can go through the specially designed Playfair cipher and be encrypted
into another DNA sequence. Then, this encrypted DNA data is randomly inserted into a reference
DNA sequence to produce a faked DNA sequence whose encrypted data is hidden.
CMC, 2022, vol.70, no.1 125
In [17] a model and implementation for key generation using the genetic algorithm with
the Needleman–Wunsch (NW) algorithm is proposed. The authors introduce a model for imple-
menting encryption and decryption based on DNA computing using the biological operations
Transcription, Translation, DNA Sequencing, and Deep Learning. They evaluate the time taken
for encryption and decryption based on the size of the message.
In [18] a Bio-Inspired Cryptosystem for encrypting data is proposed. The authors propose
a system based on the Central Dogma of Molecular Biology (CDMB) for encryption and
decryption. They used a Bidirectional Associative Memory Neural Network (BAMNN) for key
generation. Their cryptosystem shows competent encryption and decryption times even on large
data sizes when compared with other systems.
3 Proposed Model
The proposed encryption model contains three phases: the first phase is key generation in
which genetic algorithm is used to generate a random key for encryption and decryption. In the
second phase the message data is converted to amino acid throw mutable operation. in the third
phase the key generated from genetic algorithm is used to encrypt amino acid data using play
faire cypher. the three is discussed in detail as follows.
3.1 First Phase: Key Generation
Genetic algorithms will be used to generate a random key in the encryption process as follows:
3.1.1 Initial Population (Generation 0)
The genes of the chromosomes of the initial population will be filled using a random number
function that returns (1 or 0). Each chromosome will contain 64 genes and the initial population
will contain 100 chromosomes.
3.1.2 Fitness Function
The key in the encryption process must be random to ensure a low guessing factor, so the
Run Test of Randomness will be used as the fitness function in our algorithm.
3.1.3 Run Test of Randomness
The Run Test of Randomness is a statistical test that is used to calculate the randomness of
data. This test is based on the run. Run is basically a sequence of two types of symbols, such as
0 or 1. The test statistic can be calculated by using an approximation of the normal distribution
via the following formula as shown in Eq. (1).
r−μ
Z= (1)
σ
where r is the number of runs, μ is the expected number of runs, and σ is the standard deviation
of the number of runs. The values of μ and σ are computed as in Eqs. (2) and (3).
2n1 n2
μ= +1 (2)
n1 + n2
(2n1 n2 )(2n1 n2 − n1 − n2 )
σ= (3)
(n1 + n2 )2 (n1 + n2 − 1)
126 CMC, 2022, vol.70, no.1
where n1 is number of zeros in our model and n2 is number of ones in the proposed model. An
example of how to calculate the value of randomness can be found in Fig. 1.
Figure 1: An example of how to calculate the value of randomness
3.1.4 Selection
The selection policy determines which individuals are to be kicked out and which are to be
kept in the next generation to be mated and combined to create offspring. A selection policy
based on the fitness function is applied to choose which individuals to use.
3.1.5 Crossover
Crossover is used to combine the genetic information of two parents’ offspring to generate
new offspring. The K-Point is used to determine the crossover. K-Point crossover uses more
than one crossover point to produce two offspring chromosomes. Two parent chromosomes are
selected and a number is generated at random because the number of crossover points is randomly
selected. This is shown in Fig. 2.
Figure 2: Crossover selectionCMC, 2022, vol.70, no.1 127
3.1.6 Mutation
A mutation is a small random tweak in the chromosome, to get a new solution. Bit string
mutations are used as mutation operators. Bit string mutation works by selecting one or more
random bits and flipping them, see Fig. 3 below.
Figure 3: Mutation process
After choosing the best key using the fitness function, this key’s similarity to other keys from
the last generation is calculated using the Needleman-Wunsch (NW) Algorithm.
3.1.7 Needleman-Wunsch (NW) Algorithm
The Needleman-Wunsch (NW) Algorithm is a dynamic programming application. It is used
for arranging two or more sequences of characters to identify regions of similarity [17]. It uses a
scoring system to calculate the degree of similarity or dissimilarity between the two sequences. The
greater the score, the more similar the sequences. NW is used to calculate the similarity between
the chosen key and other keys from the last generation. The less similar key is selected to be the
encryption key. The key generation process is summarized in Fig. 4.
3.2 Second Phase: Data Preparation
The plain data is converted to 8-bit binary format, and then converted to a DNA Nitrogen
Base sequence as shown in Tab. 1. Then the DNA Nitrogen Base sequence is converted to an
RNA Nitrogen Base as shown in Tab. 2. The RNA Nitrogen Base is then converted to an amino
acid according to RNA to Amino Acid table in [15], and then the Ambiguity number as Protein
Key (PK) is extracted. The same model will be applied to the generated key.
3.3 Third Phase: Data Encryption Using Amino Acid Based Playfair
Playfair is a polyalphabetic cipher, in which diagrams in plaintext are treated as single units
and these units are translated into cipher text diagrams. Playfair encrypts pairs of letters, rather
than encrypting single letters as a simple substitution cipher would do. The traditional Playfair
algorithm is based on a 5 × 5 matrix of letters constructed using a key. The Playfair cipher is a
great advance over simple monoalphabetic ciphers. Cryptanalysis of the Playfair cipher is much
more difficult than cryptanalysis of normal simple substitution ciphers, because digraphs (pairs of
letters) are being substituted instead of monographs (single letters) [15].
In our model, the key generated from the genetic algorithm is used as a Playfair cipher
key, and the alphabet is the modified amino acid alphabet. The data preparation phase and the
encryption phase are summarized in Fig. 5. Also, a simple example of our proposed algorithm is
shown in Fig. 6. The algorithm steps of the encryption process are shown as follows.128 CMC, 2022, vol.70, no.1
Figure 4: The key generation processes
Table 1: Converting 8-bit binary format to DNA
DNA nitrogen base Binary sequence
A 01
C 00
G 11
T 10
Table 2: Converting DNA to RNA
DNA nitrogen base RNA nitrogen base
A A
C C
G G
T UCMC, 2022, vol.70, no.1 129
Algorithm 1: Algorithm of encryption process
Input: Message (M), Genetic KEY (GK)
Output: Protein Cypher (PC), Protein Key (PK)
Begin
1. Step 1: Input Message (M), Genetic KEY (K1).
2. Step 2: Convert Message (M) to 8-bit binary format (biM).
3. Step 3: Convert binary Message (bim M) to DNA Nitrogen Base (MDNA).
4. Step 4: Convert Message DNA Nitrogen Base (MDNA) to RNA Nitrogen Base (MRNA).
5. Step 5: Convert Message RNA Nitrogen Base (MRNA) to Protein (PM) and save protein
Ambiguity number as Protein Key (PK).
6. Step 6: Create Playfair 5 × 5 matrix and use Genetic KEY (GK) as Key.
7. Step 7: Use Playfair encryption process to get Protein Cypher (PC)
8. Step 8: Protein Ambiguity number as Protein Key (PK) and Protein Cypher (PC).
End
Figure 5: Encryption algorithm130 CMC, 2022, vol.70, no.1
Figure 6: Simple example of proposed algorithm
4 Simulation and Performance Analysis
This section presents the experimental results of the proposed model. In addition, a compar-
ison between the proposed model and Genetic Algorithm with NW model [17] is included in this
section. All the models were implemented on a PC with a Pentium core i7 processor, 8 GB of
RAM, and the Windows 10 operating system. Python was used to implement both the proposed
models and the Kalsi et al. model.
4.1 Encryption Time
The encryption time is the amount of time each model takes to generate cypher text after
generating the key. Tab. 3 compares the encryption times (in milliseconds) of the proposed model
and Genatic Algorithem with NW [17] model. The results show that our proposed model takes
slightly more time than Genatic Algorithem with NW model, because in Genatic Algorithem (GA)
with NW model the main operation is XOR but in our model the Playfair matrix takes more time
to encrypt.CMC, 2022, vol.70, no.1 131
Table 3: Comparison of encryption time with the characters from the proposed model with the
existing scheme
Total number of characters Encryption time
Genatic algorithem with NW [17] Proposed
500 0.0076003 0.063901901
1000 0.0100408 0.174080372
1500 0.0112293 0.286720276
4.2 Decryption Time
The decryption time is the amount of time each model takes to generate plain text from
cypher text. Tab. 4 compares the decryption time (in milliseconds) of the proposed model and
Genatic Algorithem with NW [17] model. The results show that our proposed model takes slightly
more time than GA with NW model, because in GA with NW [17] model the main operation is
XOR but in our model the Playfair matrix takes more time to encrypt.
Table 4: Comparison of decryption time with the characters from the proposed model with the
existing scheme
Total number of characters Encryption time
Genatic algorithem with NW [17] Proposed
500 0.0077 0.0620
1000 0.0101 0.1679
1500 0.0113 0.2487
4.3 Performance Analysis
4.3.1 Confusion and Diffusion
Confusion means that each bit of ciphertext should depend on several bits of the key. In the
proposed model, when a message is translated to protein, the process is one-to-many, because one
protein can come from more than one RNA. Also, in the proposed model if we use the key and
plaintext independently, the cipher text can’t be produced because it goes through several steps.
Diffusion means that if a change happens in one character of the plaintext, it changes several
characters in the ciphertext. In the proposed model, when a character of the plaintext is changed
it will affect the DNA value, which in turn will affect the protein value and the cipher text. Also,
in the proposed model, the same plaintext will result in different cipher text each time because
we use a different key each time.
4.3.2 Avalanche Effect
In cryptography, the avalanche effect means that if a character in plaintext is changed slightly,
the cipher text changes significantly. In the proposed model, when a character of the plaintext is
changed slightly it will affect the DNA value, which in turn will give a different protein value and
change the cipher text.132 CMC, 2022, vol.70, no.1
4.4 Security Against Attacks
4.4.1 Brute-Force Attack
A brute force attack is an attempt to crack a password or username, find a hidden web
page, or find the key used to encrypt a message, using a trial-and-error approach, and hoping,
eventually, to guess correctly [19].
4.4.2 Ciphertext-Only Attack
In a ciphertext-only attack, the attacker has access to some amount of ciphertext and has
some information about the plaintext. This type of attack will succeed if the attacker can get
either the plaintext or the key. In the proposed system this is impossible because of the random-
ness of the key generated by the genetic algorithm. Also, in this model, the plaintext goes through
multiple steps to become ciphertext [20].
4.4.3 The Known-Plaintext Attack (KPA)
The known-plaintext attack is an attack model in which the attacker has access to both the
plaintext and the ciphertext and attempts to get the key. In the proposed system the attacker
can’t succeed because of the randomness of the key generated by the genetic algorithm. It gives
a different key each time [21].
4.4.4 Differential cryptanalysis Attack
In a differential cryptanalysis attack, the attacker gets ciphertext from a set of chosen plain-
text. In the proposed system this can’t happen because of the randomness of the key generated by
the genetic algorithm. It gives a different key each time [22]. Tab. 5 outlines the implementation
of the system proposed in relation to the multiple attacks with other systems.
Table 5: Comparison of existing scheme with proposed scheme based on several attacks
Attack Model
Echo state network [23] DES-CDMB [24] Proposed
Brute-force attack Prevention of attack Prevention of attack Prevention of attack
Ciphertext-only attack Prevention of attack – Prevention of attack
The known-plaintext Prevention of attack – Prevention of attack
attack (KPA)
Differential – Failure Prevention of attack
cryptanalysis attack
4.4.5 Achievement of CIA
Confidentiality
Confidentiality is keeping information away from unauthorized people. In the proposed system
this is achieved as all transmitted entities and parameters are encrypted [25].CMC, 2022, vol.70, no.1 133
Integrity
Integrity is the ability to ensure that data is accurate and remains unchanged. In the proposed
system this is achieved because if a change happens in the cipher text it will affect the protein
value and the DNA value, and the plaintext won’t be able to be extracted [25].
Availability
It is important to ensure that the information concerned is always readily accessible to
the authorized viewer. In the proposed system, this is achieved because it works with different
plaintext size and types [25].
5 Conclusion
An amino acid cryptosystem has been proposed that uses genetic algorithms and amino
acid cryptography for securing data. The goal of data encryption is to keep data away from
unauthorized people. In our system, the input message is encoded to an 8-bit binary format and
converted to an amino acid. A genetic algorithm is used to generate an encryption key and the
Tun Test of Randomness is used as the fitness function. The MG algorithm is used to select
the key that is the least similar to the others. The encoded message is used with Playfair using
a generated key. The proposed model can survive over known attacks such as the Brute-force
attack and the Ciphertext-only attack. The proposed model has been tested over different types
of characters including white spaces and special characters as all the data is encoded to 8-bit
binary. The performance of the proposed model is compared with other models on the basis of
encryption time. The CIA principle is achieved by the proposed model. Also, using the amino
acid ambiguity number gives us more security because even if the intruder knows the input of
plaintext, he can’t know the real message without using the ambiguity number.
Funding Statement: The authors received no specific funding for this study.
Conflicts of Interest: The authors declare that they have no conflicts of interest to report regarding
the present study.
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